asmariyaz23

"Wrapper passed wrong version number" error (Seurat v2)

4

Hello, I tried to install and run fast_tsne in bin folder, but it fails saying the following everytime: =============== t-SNE v1.1.0 =============== Wrapper passed wrong version number: --version Could you...

scRNA-seq: how to create the Ranked list?

19

Hello, I have some clusters with differentially expresses genes generated using Seurat. I also have a highly curated gene list and I wish to perform enrichment analysis using these on...

Hello, I am writing to request for the addition of Trinity Cancer Transcriptome Analysis Toolkit (CTAT) tools to Galaxy main. These tools leverage RNA-Seq to gain insights into the biology...

Hello, I am new to deepTools and want to run computeMatrix (twice) to study gene promoter effect during activation on 1 mark (H3K4me3) by comparing 2 cell types: 1) activated...

emapplot 'x' must be an array of at least two dimensions

1

Hello, I am trying to use emapplot and get the following error: ``` emapplot(GO_CC_down) + labs(title="Enrichment map for GO CC down") + theme(plot.title=element_text(hjust=0.5,size=15,face="bold")) Error in rowSums(data[, cols]) : 'x' must...

High memory and runtime requirements when adding scRNA-seq data

3

Hello, I’m trying to run Segger with the tutorial data. The pipeline runs fine (with reasonable memory and runtime) when I exclude the scRNA-seq data, but when I include it,...

Hello, I am trying to run cnvkit in the following steps, for context I have tumor only samples from WES dataset: ``` cnvkit.py \ antitarget \ intervals_sorted.bed \ --output intervals.antitarget.bed...